Small functions that are useful not only for one modul. More...

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "config.h"
#include "debug.h"
#include "errorhandling.h"

Include dependency graph for utils.h:

Go to the source code of this file.

Data Structures
struct	IntList
	Integer list. More...
struct	DoubleList
	Double list. More...
Defines
#define	PMASS(pt) (pt).p.mass
	macro for easy use of mass.
#define	AS_a1 0.254829592
#define	AS_a2 -0.284496736
#define	AS_a3 1.421413741
#define	AS_a4 -1.453152027
#define	AS_a5 1.061405429
#define	AS_p 0.3275911
#define	epsi 0.1
#define	c2 -0.1666666666667e-0
#define	c4 0.8333333333333e-2
#define	c6 -0.1984126984127e-3
#define	c8 0.2755731922399e-5
Mathematical, physical and chemical constants.
#define	PI 3.14159265358979323846264338328
	Pi.
#define	wupi 1.77245385090551602729816748334
	Square root of Pi.
#define	wupii 0.56418958354775627928034964498
	One over square root of Pi.
#define	driwu2 1.25992104989487316476721060728
	Pi to the power 1/3.
#define	ES_OK 0
	error code if no error occured
#define	ES_ERROR 1
	error code if an error occured
#define	ES_INTEGER_SPACE 24
	space necessary for an (64-bit) integer with sprintf.
#define	ES_DOUBLE_SPACE 27
	space necessary for an double with sprintf.
Functions
Mathematical functions.
MDINLINE double	dmax (double a, double b)
	Calculates the maximum of 'double'-typed a and b, returning 'double'.
MDINLINE double	dmin (double a, double b)
	Calculates the minimum of 'double'-typed a and b, returning 'double'.
MDINLINE int	imax (int a, int b)
	Calculates the maximum of 'int'-typed a and b, returning 'int'.
MDINLINE int	imin (int a, int b)
	Calculates the minimum of 'int'-typed a and b, returning 'int'.
MDINLINE double	drem_down (double a, double b)
	Calculates the remainder of a division.
MDINLINE void	vector_subt (double res[3], double a[3], double b[3])
	vector difference
MDINLINE void	sort_int_array (int *data, int size)
	Very slow sort routine for small integer arrays.
MDINLINE void	permute_ifield (int *field, int size, int permute)
	permute an interger array field of size size about permute positions.
MDINLINE double	dround (double x)
	Mathematically rounds 'double'-typed x, returning 'double'.
MDINLINE double	SQR (double x)
	Calculates the SQuaRe of 'double' x, returning 'double'.
MDINLINE double	AS_erfc_part (double d)
	approximates $\exp(d^2) \mathrm{erfc}(d)$ by applying a formula from: Abramowitz/Stegun: Handbook of Mathematical Functions, Dover (9.
MDINLINE double	sinc (double d)
	Calculates the sinc-function as sin(PIx)/(PIx).
MDINLINE int	calc_factors (int n, int *factors, int max)
	factorizes small numbers up to a maximum of max factors.
Vector and matrix operations for three dimensons.
MDINLINE void	vecsub (double v1[3], double v2[3], double dv[3])
	Subtracts vector v2 from vector v1 and stores resuld in vector dv.
MDINLINE double	normr (double v[3])
	calculates the length of a vector
MDINLINE double	sqrlen (double v[3])
	calculates the squared length of a vector
MDINLINE void	unit_vector (double v[3], double y[3])
	calculates unit vector
MDINLINE double	scalar (double a[3], double b[3])
	calculates the scalar product of two vectors a nd b
MDINLINE void	vector_product (double a[3], double b[3], double c[3])
	calculates the vector product c of two vectors a and b
MDINLINE void	vec_rotate (double axis, double alpha, double vector, double *result)
	rotates vector around axis by alpha
MDINLINE int	calc_eigenvalues_3x3 (double q, double eva)
	Calc eigevalues of a 3x3 matrix stored in q as a 9x1 array.
MDINLINE int	calc_eigenvector_3x3 (double a, double eva, double eve)
	Calc eigevectors of a 3x3 matrix stored in a as a 9x1 array.
Linear algebra functions
MDINLINE int	lu_decompose_matrix (double *A, int n, int perms)
	Calculate the LU decomposition of a matrix A.
MDINLINE void	lu_solve_system (double *A, int n, int perms, double *b)
	Solve the linear equation system for a LU decomposed matrix A.
Three dimensional grid operations
MDINLINE int	get_linear_index (int a, int b, int c, int adim[3])
	get the linear index from the position (a,b,c) in a 3D grid of dimensions adim[].
MDINLINE void	get_grid_pos (int i, int a, int b, int *c, int adim[3])
	get the position a[] from the linear index in a 3D grid of dimensions adim[].
MDINLINE int	malloc_3d_grid (double ****grid, int dim[3])
	Malloc a 3d grid for doubles with dimension dim[3] .
MDINLINE void	print_block (double *data, int start[3], int size[3], int dim[3], int element, int num)
	print a block of a 3D array.
Distance calculations.
MDINLINE double	distance (double pos1[3], double pos2[3])
	returns the distance between two position.
MDINLINE double	distance2 (double pos1[3], double pos2[3])
	returns the distance between two positions squared.
MDINLINE double	distance2vec (double pos1[3], double pos2[3], double vec[3])
	Returns the distance between two positions squared and stores the distance vector pos1-pos2 in vec.
MDINLINE double	unfolded_distance (double pos1[3], int image_box1[3], double pos2[3], int image_box2[3], double box_l[3])
	returns the distance between the unfolded coordintes of two particles.
String helper functions
MDINLINE char *	strcat_alloc (char left, char right)
	extend a string with another one.
Object-in-fluid functions
MDINLINE double	area_triangle_new (double P1, double P2)
	Computes the area of triangle between vectors P1 and P2, by computing the crossproduct P1 x P2 and taking the half of its norm.
MDINLINE double	area_triangle (double P1, double P2, double *P3)
	Computes the area of triangle between vectors P1,P2,P3, by computing the crossproduct P1P2 x P1P3 and taking the half of its norm.
MDINLINE void	get_n_triangle (double p1, double p2, double p3, double n)
	Computes the normal vector to the plane given by points P1P2P3.
MDINLINE double	angle_btw_triangles (double P1, double P2, double P3, double P4)
	This function returns the angle btw the triangle p1,p2,p3 and p2,p3,p4.
List operations .
int	this_node
	The number of this node.
MDINLINE void	init_intlist (IntList *il)
	Initialize an IntList.
MDINLINE void	alloc_intlist (IntList *il, int size)
	Allocate an IntList of size size.
MDINLINE void	realloc_intlist (IntList *il, int size)
	Reallocate an IntList.
MDINLINE void	alloc_grained_intlist (IntList *il, int size, int grain)
	Allocate an IntList, but only to multiples of grain.
MDINLINE void	realloc_grained_intlist (IntList *il, int size, int grain)
	Reallocate an IntList, but only to multiples of grain.
MDINLINE int	intlist_contains (IntList *il, int c)
	Check wether an IntList contains the value c.
MDINLINE void	init_doublelist (DoubleList *il)
	Initialize an DoubleList.
MDINLINE void	alloc_doublelist (DoubleList *dl, int size)
	Allocate an DoubleList of size size.
MDINLINE void	realloc_doublelist (DoubleList *dl, int size)
	Reallocate an DoubleList.
MDINLINE void	alloc_grained_doublelist (DoubleList *dl, int size, int grain)
	Allocate an DoubleList, but only to multiples of grain.
MDINLINE void	realloc_grained_doublelist (DoubleList *dl, int size, int grain)
	Reallocate an DoubleList, but only to multiples of grain.

Detailed Description

Small functions that are useful not only for one modul.

just some nice utilities... and some constants...

Definition in file utils.h.

Define Documentation

#define AS_a1 0.254829592

Referenced by AS_erfc_part().

#define AS_a2 -0.284496736

Referenced by AS_erfc_part().

#define AS_a3 1.421413741

Referenced by AS_erfc_part().

#define AS_a4 -1.453152027

Referenced by AS_erfc_part().

#define AS_a5 1.061405429

Referenced by AS_erfc_part().

#define AS_p 0.3275911

Referenced by AS_erfc_part().

#define c2 -0.1666666666667e-0

Referenced by sinc().

#define c4 0.8333333333333e-2

Referenced by sinc().

#define c6 -0.1984126984127e-3

Referenced by sinc().

#define c8 0.2755731922399e-5

Referenced by sinc().

#define driwu2 1.25992104989487316476721060728

Pi to the power 1/3.

Definition at line 49 of file utils.h.

Referenced by lj_cos_set_params().

#define epsi 0.1

Referenced by sinc().

#define ES_DOUBLE_SPACE 27

space necessary for an double with sprintf.

Precision is 17 digits, plus sign, dot, e, sign of exponent and 3 digits exponent etc. Analog to Tcl

Definition at line 64 of file utils.h.

Referenced by analyze_fold_molecules(), dd_create_cell_grid(), dd_position_to_cell(), dp3m_adaptive_tune(), dp3m_mc_time(), dp3m_sanity_checks_boxl(), fold_coordinate(), layered_exchange_and_sort_particles(), layered_topology_init(), mmm1d_tune(), p3m_adaptive_tune(), p3m_mc_time(), p3m_sanity_checks_boxl(), propagate_press_box_pos_and_rescale_npt(), and tclprint_to_result_comfixedIA().

#define ES_ERROR 1

error code if an error occured

Definition at line 54 of file utils.h.

#define ES_INTEGER_SPACE 24

space necessary for an (64-bit) integer with sprintf.

Analog to Tcl

Definition at line 59 of file utils.h.

Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_constraints_energy(), add_constraints_forces(), add_three_body_bonded_stress(), add_volume_force(), analyze_activate(), analyze_fold_molecules(), calc_area_global(), calc_bonded_force(), calc_local_mol_info(), calc_mol_info(), calc_mol_pos(), calc_mol_vel(), calc_three_body_bonded_forces(), calc_trap_force(), calc_volume(), change_particle_bond(), compute_pos_corr_vec(), compute_vel_corr_vec(), correct_pos_shake(), dd_create_cell_grid(), dd_on_geometry_change(), distribute_tensors(), dp3m_adaptive_tune(), dp3m_mc_time(), fene_pair_energy(), fold_coordinate(), get_local_trapped_mols(), get_mol_com_particle(), get_mol_dist(), getintersection(), handle_collisions(), layered_topology_init(), local_stress_tensor_calc(), map_to_2dgrid(), meta_init(), meta_perform(), mindist3(), mmm1d_tune(), nemd_change_momentum(), p3m_adaptive_tune(), p3m_mc_time(), print_bond_len(), put_mol_force_on_parts(), update_mol_pos_particle(), update_mol_vel_particle(), and vs_relate_to().

#define ES_OK 0

error code if no error occured

Definition at line 52 of file utils.h.

Referenced by add_particle_to_list(), analyze_fold_molecules(), angle_cosine_set_params(), angle_cossquare_set_params(), angle_harmonic_set_params(), angle_set_params(), angledist_set_params(), area_force_global_set_params(), area_force_local_set_params(), bending_force_set_params(), BMHTF_set_params(), buckingham_set_params(), calc_radial_density_map(), change_exclusion(), comfixed_set_params(), coulomb_set_bjerrum(), cuda_check_gpu(), cuda_set_device(), dawaanr_set_params(), delete_particle_of_type(), dihedral_set_params(), dipolar_set_Dbjerrum(), dp3m_adaptive_tune(), dp3m_set_eps(), dp3m_set_mesh_offset(), dp3m_set_ninterpol(), ELC_set_params(), ELC_tune(), endangledist_set_params(), fene_set_params(), find_particle_type(), find_particle_type_id(), forcecap_set_params(), free_particle_lists(), gather_runtime_errors(), gaussian_set_params(), gay_berne_set_params(), gc_status(), get_particle_data(), gpu_init_particle_comm(), harmonic_set_params(), hat_set_params(), hertzian_set_params(), init_gc(), init_type_array(), inter_dpd_set_params(), interrf_set_params(), lb_lbfluid_load_checkpoint(), lb_lbfluid_save_checkpoint(), lb_lbnode_set_extforce_GPU(), lbnode_parse_set(), lennard_jones_set_params(), list_gpus(), lj_cos_set_params(), ljangle_set_params(), ljcos2_set_params(), ljforcecap_set_params(), ljgen_set_params(), local_change_bond(), maggs_set_parameters(), mdds_set_params(), mdlc_set_params(), mdlc_tune(), mmm1d_tune(), MMM2D_set_params(), molcut_set_params(), morse_set_params(), mpi_gather_runtime_errors(), nemd_free(), number_of_particles_with_type(), orient_order(), p3m_adaptive_tune(), p3m_set_eps(), p3m_set_mesh_offset(), p3m_set_ninterpol(), reallocate_global_type_list(), reallocate_type_array(), remove_id_type_array(), remove_particle(), rigid_bond_set_params(), set_molecule_trap(), set_particle_dip(), set_particle_dipm(), set_particle_ext_force(), set_particle_ext_torque(), set_particle_f(), set_particle_fix(), set_particle_gamma(), set_particle_mass(), set_particle_mol_id(), set_particle_mu_E(), set_particle_omega_body(), set_particle_omega_lab(), set_particle_q(), set_particle_quat(), set_particle_rotation(), set_particle_rotational_inertia(), set_particle_solvation(), set_particle_temperature(), set_particle_torque_body(), set_particle_torque_lab(), set_particle_type(), set_particle_v(), set_particle_virtual(), set_particle_vs_relative(), smooth_step_set_params(), soft_sphere_set_params(), stretching_force_set_params(), subt_lj_set_params(), tabulated_bonded_set_params(), tclcommand_cuda(), tclcommand_inter_coulomb_parse_maggs(), tclcommand_inter_coulomb_parse_mmm1d(), tclcommand_inter_magnetic_parse_dawaanr(), tclcommand_inter_magnetic_parse_mdds(), tf_set_params(), try_delete_bond(), tunable_slip_set_params(), update_particle_array(), virtual_set_params(), volume_force_set_params(), and vs_relate_to().

#define PI 3.14159265358979323846264338328

Pi.

Definition at line 43 of file utils.h.

Referenced by adress_wf(), Aliasing_sums_ik(), analyze_rdfchain(), apply_diff_op(), build_verlet_lists(), build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calc_angledist_param(), calc_cell_gpb(), calc_dihedral_angle(), calc_dihedral_force(), calc_endangledist_pair_force(), calc_radial_density_map(), calc_rdf(), calc_rdf_adress(), calc_rdf_av(), calc_rdf_intermol_av(), calc_structurefactor(), calc_wallrdfyz(), calculate_influence_function(), convert_quatu_to_quat(), dp3m_average_dipolar_self_energy(), dp3m_calc_kspace_forces(), dp3m_compute_constants_energy_dipolar(), dp3m_k_space_error(), dp3m_perform_aliasing_sums_energy(), dp3m_perform_aliasing_sums_force(), dp3m_tune_aliasing_sums(), endangledist_pair_energy(), lj_cos_set_params(), maxwell_velocitiesC(), mdlc_tune(), observable_radial_density_profile(), observable_radial_flux_density_profile(), observable_structure_factor(), p3m_analytic_cotangent_sum(), p3m_calc_influence_function_energy(), p3m_calc_influence_function_force(), p3m_calc_kspace_forces(), p3m_calc_kspace_stress(), p3m_perform_aliasing_sums_energy(), p3m_perform_aliasing_sums_force(), p3m_tune_aliasing_sums(), polymerC(), sinc(), tabulated_bonded_set_params(), tclcommand_analyze_parse_structurefactor(), tclcommand_inter_parse_angle(), tclcommand_inter_parse_angle_cosine(), tclcommand_inter_parse_angle_cossquare(), tclcommand_inter_parse_angle_harmonic(), tclcommand_parse_radial_profile(), and tclcommand_polymer().

#define PMASS ( pt ) (pt).p.mass

macro for easy use of mass.

If masses are not switched on, the particle mass is defined to 1, so it should be compiled out in most cases.

Definition at line 163 of file utils.h.

Referenced by add_dpd_thermo_pair_force(), add_inter_dpd_pair_force(), add_kinetic_energy(), add_kinetic_virials(), analyze_rdfchain(), angularmomentum(), calc_comfixed(), calc_energy_kinetic_mol(), calc_g123(), calc_g2_av(), calc_g3_av(), calc_kinetic(), calc_local_mol_info(), calc_local_temp(), calc_mol_center_of_mass(), calc_mol_gyr_radius2(), calc_mol_pos(), calc_mol_pos_cfg(), calc_mol_vel(), calc_rg(), calc_rg_av(), centermass(), centermass_conf(), compute_pos_corr_vec(), compute_vel_corr_vec(), friction_thermo_langevin(), init_g123(), local_stress_tensor_calc(), momentofinertiamatrix(), observable_blocked_com_position(), observable_blocked_com_velocity(), observable_com_position(), observable_com_velocity(), partial_momentum_update(), propagate_vel(), put_mol_force_on_parts(), rescale_forces(), rescale_forces_propagate_vel(), simple_momentum_update(), and tclcommand_analyze_parse_and_print_energy_kinetic().

#define wupi 1.77245385090551602729816748334

Square root of Pi.

Definition at line 45 of file utils.h.

#define wupii 0.56418958354775627928034964498

One over square root of Pi.

Definition at line 47 of file utils.h.

Referenced by dp3m_add_pair_force(), dp3m_calc_kspace_forces(), dp3m_compute_constants_energy_dipolar(), dp3m_pair_energy(), p3m_add_pair_force(), and p3m_calc_kspace_forces().

Function Documentation

MDINLINE void alloc_doublelist	(	DoubleList *	dl,
		int	size
	)

Allocate an DoubleList of size size.

If you need an DoubleList with variable size better use realloc_doublelist

Definition at line 238 of file utils.h.

References DoubleList::e, malloc, and DoubleList::max.

Referenced by mpi_local_stress_tensor(), mpi_local_stress_tensor_slave(), parse_corr_operation(), preparePolygammaEven(), tclcommand_analyze_parse_bilayer_density_profile(), tclcommand_analyze_parse_local_stress_tensor(), tclcommand_analyze_parse_radial_density_map(), and tclcommand_bin().

MDINLINE void alloc_grained_doublelist	(	DoubleList *	dl,
		int	size,
		int	grain
	)

Allocate an DoubleList, but only to multiples of grain.

Definition at line 254 of file utils.h.

References DoubleList::e, malloc, and DoubleList::max.

MDINLINE void alloc_grained_intlist	(	IntList *	il,
		int	size,
		int	grain
	)

Allocate an IntList, but only to multiples of grain.

Definition at line 200 of file utils.h.

References IntList::e, malloc, and IntList::max.

MDINLINE void alloc_intlist	(	IntList *	il,
		int	size
	)

Allocate an IntList of size size.

If you need an IntList with variable size better use realloc_intlist

Definition at line 184 of file utils.h.

References IntList::e, malloc, and IntList::max.

Referenced by calc_vanhove(), check_cells_consistency(), mpi_recv_part(), parse_id_list(), recv_particles(), tclcommand_analyze_parse_holes(), tclcommand_analyze_parse_radial_density_map(), and tclcommand_analyze_set_parse_trapmol().

MDINLINE double angle_btw_triangles	(	double *	P1,
		double *	P2,
		double *	P3,
		double *	P4
	)

This function returns the angle btw the triangle p1,p2,p3 and p2,p3,p4.

Be careful, the angle depends on the orientation of the trianlges! You need to be sure that the orientation (direction of normal vector) of p1p2p3 is given by the cross product p2p1 x p2p3. The orientation of p2p3p4 must be given by p2p3 x p2p4.

Example: p1 = (0,0,1), p2 = (0,0,0), p3=(1,0,0), p4=(0,1,0). The orientation of p1p2p3 should be in the direction (0,1,0) and indeed: p2p1 x p2p3 = (0,0,1)x(1,0,0) = (0,1,0) This function is called in the beginning of the simulation when creating bonds depending on the angle btw the triangles, the bending_force. Here, we determine the orientations by looping over the triangles and checking the correct orientation. So when defining the bonds by tcl command "part p2 bond xxxx p1 p3 p4", we correctly input the particle id's. So if you have the access to the order of particles, you are safe to call this function with exactly this order. Otherwise you need to check the orientations.

Definition at line 991 of file utils.h.

References M_PI, scalar(), sqrlen(), and vector_product().

Referenced by calc_bending_force().

MDINLINE double area_triangle	(	double *	P1,
		double *	P2,
		double *	P3
	)

Computes the area of triangle between vectors P1,P2,P3, by computing the crossproduct P1P2 x P1P3 and taking the half of its norm.

Definition at line 953 of file utils.h.

References normr(), and vector_product().

Referenced by add_volume_force(), calc_area_force_local(), calc_area_global(), and calc_volume().

MDINLINE double area_triangle_new	(	double *	P1,
		double *	P2
	)

Computes the area of triangle between vectors P1 and P2, by computing the crossproduct P1 x P2 and taking the half of its norm.

Definition at line 942 of file utils.h.

References normr(), and vector_product().

Referenced by calc_area_force_local_complicated().

MDINLINE double AS_erfc_part ( double d )

approximates $\exp(d^2) \mathrm{erfc}(d)$ by applying a formula from: Abramowitz/Stegun: Handbook of Mathematical Functions, Dover (9.

ed.), chapter 7

Definition at line 343 of file utils.h.

References AS_a1, AS_a2, AS_a3, AS_a4, AS_a5, and AS_p.

Referenced by dp3m_add_pair_force(), dp3m_pair_energy(), p3m_add_pair_force(), and p3m_pair_energy().

MDINLINE int calc_eigenvalues_3x3	(	double *	q,
		double *	eva
	)

Calc eigevalues of a 3x3 matrix stored in q as a 9x1 array.

Definition at line 492 of file utils.h.

Referenced by calc_comforce(), calc_gyration_tensor(), and tclcommand_analyze_parse_find_principal_axis().

MDINLINE int calc_eigenvector_3x3	(	double *	a,
		double	eva,
		double *	eve
	)

Calc eigevectors of a 3x3 matrix stored in a as a 9x1 array.

Given an eigenvalue (eva) returns the corresponding eigenvector (eve)

Definition at line 552 of file utils.h.

References i.

Referenced by calc_comforce(), calc_gyration_tensor(), and tclcommand_analyze_parse_find_principal_axis().

MDINLINE int calc_factors	(	int	n,
		int *	factors,
		int	max
	)

factorizes small numbers up to a maximum of max factors.

Definition at line 390 of file utils.h.

References i.

MDINLINE double distance	(	double	pos1[3],
		double	pos2[3]
	)

returns the distance between two position.

Parameters:

pos1	Position one.
pos2	Position two.

Definition at line 859 of file utils.h.

References SQR().

Referenced by add_partner(), adress_dw_dir(), adress_wf_vector(), auto_exclusion(), calc_vanhove(), lipid_orientation(), tclcommand_analyze_parse_and_print_check_mol(), tclcommand_part_parse_print(), and tclcommand_part_print_bond_partners().

MDINLINE double distance2	(	double	pos1[3],
		double	pos2[3]
	)

returns the distance between two positions squared.

Parameters:

pos1	Position one.
pos2	Position two.

Definition at line 868 of file utils.h.

References SQR().

Referenced by build_verlet_lists(), check_resort_particles(), clusters_connected(), propagate_pos(), propagate_vel_pos(), and tclcommand_analyze_print_MSD().

MDINLINE double distance2vec	(	double	pos1[3],
		double	pos2[3],
		double	vec[3]
	)

Returns the distance between two positions squared and stores the distance vector pos1-pos2 in vec.

Parameters:

pos1	Position one.
pos2	Position two.
vec	vecotr pos1-pos2.

Returns:: distance squared

Definition at line 880 of file utils.h.

References SQR().

Referenced by build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calc_link_cell(), calc_link_cell_iccp3m(), calculate_link_cell_energies(), calculate_link_cell_virials(), calculate_verlet_energies(), calculate_verlet_ia(), calculate_verlet_ia_iccp3m(), calculate_verlet_virials(), and detect_collision().

MDINLINE double dmax	(	double	a,
		double	b
	)

Calculates the maximum of 'double'-typed a and b, returning 'double'.

Definition at line 281 of file utils.h.

Referenced by determine_bessel_cutoff(), MMM2D_tune_near(), tclcommand_crosslink(), tclcommand_metadynamics_parse_distance(), and tclcommand_metadynamics_parse_relative_z().

MDINLINE double dmin	(	double	a,
		double	b
	)

Calculates the minimum of 'double'-typed a and b, returning 'double'.

Definition at line 284 of file utils.h.

Referenced by buf_mindist4(), calc_minimal_box_dimensions(), dd_create_cell_grid(), dd_on_geometry_change(), distto(), dp3m_adaptive_tune(), dp3m_mc_time(), ELC_init(), ELC_set_params(), ELC_tune(), mindist(), mindist4(), MMM2D_tune_far(), p3m_adaptive_tune(), p3m_mc_time(), tclcommand_metadynamics_parse_distance(), and tclcommand_metadynamics_parse_relative_z().

MDINLINE double drem_down	(	double	a,
		double	b
	)

Calculates the remainder of a division.

Definition at line 293 of file utils.h.

Referenced by distribute_tensors(), getintersection(), getlength(), and local_stress_tensor_calc().

MDINLINE double dround ( double x )

Mathematically rounds 'double'-typed x, returning 'double'.

Definition at line 335 of file utils.h.

Referenced by add_ljangle_pair_force(), buf_mindist4(), calc_dihedral_angle(), crosslinkC(), distribute_tensors(), dp3m_calc_differential_operator(), dp3m_calc_meshift(), get_mi_vector(), layered_get_mi_vector(), ljangle_pair_energy(), meta_perform(), mindist3(), and mindist4().

MDINLINE void get_grid_pos	(	int	i,
		int *	a,
		int *	b,
		int *	c,
		int	adim[3]
	)

get the position a[] from the linear index in a 3D grid of dimensions adim[].

Parameters:

i	linear index
a	x position (return value)
b	y position (return value)
c	z position (return value)
adim	dimensions of the underlying grid

Definition at line 777 of file utils.h.

References i.

Referenced by cluster_neighbors().

MDINLINE int get_linear_index	(	int	a,
		int	b,
		int	c,
		int	adim[3]
	)

get the linear index from the position (a,b,c) in a 3D grid of dimensions adim[].

returns linear index.

Returns:: the linear index

Parameters:

a	x position
b	y position
c	z position
adim	dimensions of the underlying grid

Definition at line 763 of file utils.h.

Referenced by cluster_neighbors(), dd_append_particles(), dd_fill_comm_cell_lists(), dd_init_cell_interactions(), dd_position_to_cell(), dd_save_position_to_cell(), dfft_init(), fft_find_comm_groups(), fft_init(), halo_push_communication(), init_lattice(), lb_bounce_back(), lb_calc_densprof(), lb_calc_fluid_mass(), lb_calc_fluid_momentum(), lb_calc_fluid_temp(), lb_calc_n_from_modes_push(), lb_calc_velprof(), lb_check_halo_regions(), lb_init_boundaries(), lb_lbnode_get_boundary(), lb_lbnode_get_pi_neq(), lb_lbnode_get_pop(), lb_lbnode_get_rho(), lb_lbnode_get_u(), lb_lbnode_set_pop(), lb_lbnode_set_rho(), lb_lbnode_set_u(), and map_position_to_lattice().

MDINLINE void get_n_triangle	(	double *	p1,
		double *	p2,
		double *	p3,
		double *	n
	)

Computes the normal vector to the plane given by points P1P2P3.

Definition at line 969 of file utils.h.

Referenced by add_volume_force(), calc_area_global(), calc_bending_force(), and calc_volume().

MDINLINE int imax	(	int	a,
		int	b
	)

Calculates the maximum of 'int'-typed a and b, returning 'int'.

Definition at line 287 of file utils.h.

Referenced by counterionsC(), fft_calc_send_block(), get_ia_param_safe(), layered_topology_init(), polymerC(), and saltC().

MDINLINE int imin	(	int	a,
		int	b
	)

Calculates the minimum of 'int'-typed a and b, returning 'int'.

Definition at line 290 of file utils.h.

Referenced by fft_calc_send_block(), fft_print_global_fft_mesh(), p3m_mc_time(), and print_block().

MDINLINE void init_doublelist ( DoubleList * il )

Initialize an DoubleList.

Definition at line 229 of file utils.h.

References DoubleList::e, DoubleList::max, and DoubleList::n.

Referenced by force_and_energy_tables_init(), mpi_local_stress_tensor(), mpi_local_stress_tensor_slave(), preparePolygammaEven(), preparePolygammaOdd(), tclcommand_analyze_parse_bilayer_density_profile(), tclcommand_analyze_parse_local_stress_tensor(), tclcommand_analyze_parse_radial_density_map(), tclcommand_analyze_set_parse_trapmol(), tclcommand_analyze_wallstuff(), tclcommand_bin(), tclcommand_metadynamics_parse_load_stat(), and tf_tables_init().

MDINLINE void init_intlist ( IntList * il )

MDINLINE int intlist_contains	(	IntList *	il,
		int	c
	)

Check wether an IntList contains the value c.

Definition at line 220 of file utils.h.

References IntList::e, i, and IntList::n.

Referenced by get_local_trapped_mols(), mindist(), and mpi_comm_mol_info().

MDINLINE int lu_decompose_matrix	(	double **	A,
		int	n,
		int *	perms
	)

Calculate the LU decomposition of a matrix A.

Uses Crout's method with partial implicit pivoting. The original matrix A is replaced by its LU decomposition. Due to the partial pivoting the result may contain row permutations which are recorded in perms.

Returns:: 0 for success, -1 otherwise (i.e. matrix is singular)

Parameters:

A	Matrix to be decomposed (Input/Output)
n	Dimension of the matrix (Input)
perms	Records row permutations effected by pivoting (Output)

Crout's algorithm: Calculate L and U columnwise from top to bottom. The diagonal elements of L are chosen to be 1. Only previously determined entries are used in the calculation. The original matrix elements are used only once and can be overwritten with the elements of L and U, the diagonal of L not being stored. Rows may be permuted according to the largest element (pivot) in the lower part, where rows are normalized to have the largest element scaled to unity.

Definition at line 628 of file utils.h.

References free, i, malloc, and max().

MDINLINE void lu_solve_system	(	double **	A,
		int	n,
		int *	perms,
		double *	b
	)

Solve the linear equation system for a LU decomposed matrix A.

Uses forward substitution for the lower triangle part and backsubstitution for the upper triangle part. Row permutations as indicated in perms are applied to b accordingly. The solution is written to b in place.

Parameters:

A	Matrix in LU decomposed form (Input)
n	Dimension of the matrix (Input)
perms	Indicates row permutations due to pivoting (Input)
b	Right-hand side of equation system (Input). Is destroyed and contains the solution x afterwards (Output).

Definition at line 722 of file utils.h.

References i.

MDINLINE int malloc_3d_grid	(	double ****	grid,
		int	dim[3]
	)

Malloc a 3d grid for doubles with dimension dim[3] .

Parameters:

grid	pointer to grid.
dim	dimension of the grid.

Definition at line 790 of file utils.h.

References i, and malloc.

MDINLINE double normr ( double v[3] )

calculates the length of a vector

Definition at line 426 of file utils.h.

References i, and SQR().

Referenced by add_area_global_force(), add_volume_force(), area_triangle(), area_triangle_new(), calc_area_force_local(), calc_area_force_local_complicated(), calc_bending_force(), and calc_volume().

MDINLINE void permute_ifield	(	int *	field,
		int	size,
		int	permute
	)

permute an interger array field of size size about permute positions.

Definition at line 320 of file utils.h.

References i.

Referenced by dfft_init(), and fft_init().

MDINLINE void print_block	(	double *	data,
		int	start[3],
		int	size[3],
		int	dim[3],
		int	element,
		int	num
	)

print a block of a 3D array.

Parameters:

data	3D array.
start	start coordinate for the block.
size	size of the block.
dim	dimension of the array.
element	size of the elements in the array.
num	number of element to print.

Definition at line 815 of file utils.h.

References imin().

MDINLINE void realloc_doublelist	(	DoubleList *	dl,
		int	size
	)

MDINLINE void realloc_grained_doublelist	(	DoubleList *	dl,
		int	size,
		int	grain
	)

Reallocate an DoubleList, but only to multiples of grain.

Definition at line 261 of file utils.h.

References DoubleList::e, DoubleList::max, and realloc.

MDINLINE void realloc_grained_intlist	(	IntList *	il,
		int	size,
		int	grain
	)

Reallocate an IntList, but only to multiples of grain.

Definition at line 207 of file utils.h.

References IntList::e, IntList::max, and realloc.

Referenced by wall_sort_particles().

MDINLINE void realloc_intlist	(	IntList *	il,
		int	size
	)

Reallocate an IntList.

Definition at line 191 of file utils.h.

References IntList::e, IntList::max, and realloc.

Referenced by add_link(), add_partner(), auto_exclusion(), calc_mol_info(), calc_vanhove(), check_cells_consistency(), collectBonds(), convert_types_to_ids(), free_particle(), freePartCfg(), get_local_trapped_mols(), local_change_bond(), local_change_exclusion(), local_remove_all_particles(), MMM2D_tune_near(), mpi_get_particles(), mpi_get_particles_slave(), mpi_sync_topo_part_info_slave(), nbhood(), orient_order(), parse_int_list(), realloc_topology(), recv_particles(), remove_all_bonds_to(), send_particles(), tclcommand_analyze_parse_bilayer_density_profile(), tclcommand_analyze_parse_generic_structure(), tclcommand_analyze_parse_get_lipid_orients(), tclcommand_analyze_parse_holes(), tclcommand_analyze_parse_nbhood(), tclcommand_analyze_parse_radial_density_map(), tclcommand_analyze_set_parse_chain_topology(), tclcommand_analyze_set_parse_trapmol(), tclcommand_part_print_bond_partners(), try_add_exclusion(), try_delete_bond(), try_delete_exclusion(), and wall_sort_particles().

MDINLINE double scalar	(	double	a[3],
		double	b[3]
	)

calculates the scalar product of two vectors a nd b

Definition at line 457 of file utils.h.

References i.

Referenced by add_ljangle_pair_force(), angle_btw_triangles(), angle_cosine_energy(), angle_cossquare_energy(), angle_energy(), angle_harmonic_energy(), angledist_energy(), calc_angle_3body_forces(), calc_angle_3body_tabulated_forces(), calc_angle_cosine_3body_forces(), calc_angle_cosine_force(), calc_angle_cossquare_3body_forces(), calc_angle_cossquare_force(), calc_angle_force(), calc_angle_harmonic_3body_forces(), calc_angle_harmonic_force(), calc_angledist_force(), calc_angledist_param(), calc_comforce(), calc_dihedral_angle(), calc_overlap_angle_force(), calc_pwangle(), calc_radial_density_map(), calc_tab_angle_force(), compute_pos_corr_vec(), compute_vel_corr_vec(), ext_magn_field_energy(), lb_apply_forces(), lb_calc_fluid_temp(), lb_calc_local_fields(), lb_calc_n_equilibrium(), lb_relax_modes(), ljangle_pair_energy(), orient_order(), overlap_angle_energy(), tab_angle_energy(), and vec_rotate().

MDINLINE double sinc ( double d )

Calculates the sinc-function as sin(PI*x)/(PI*x).

(same convention as in Hockney/Eastwood). In order to avoid divisions by 0, arguments, whose modulus is smaller than epsi, will be evaluated by an 8th order Taylor expansion of the sinc function. Note that the difference between sinc(x) and this expansion is smaller than 0.235e-12, if x is smaller than 0.1. (The next term in the expansion is the 10th order contribution PI^10/39916800 * x^10 = 0.2346...*x^12). This expansion should also save time, since it reduces the number of function calls to sin().

Definition at line 370 of file utils.h.

References c2, c4, c6, c8, epsi, PI, and SQR().

Referenced by Aliasing_sums_ik(), dp3m_perform_aliasing_sums_dipolar_self_energy(), dp3m_perform_aliasing_sums_energy(), dp3m_perform_aliasing_sums_force(), dp3m_tune_aliasing_sums(), p3m_perform_aliasing_sums_energy(), p3m_perform_aliasing_sums_force(), and p3m_tune_aliasing_sums().

MDINLINE void sort_int_array	(	int *	data,
		int	size
	)

Very slow sort routine for small integer arrays.

Sorts the values in decending order.

Parameters:

data	the integer array
size	size of the array

Definition at line 308 of file utils.h.

References i.

MDINLINE double SQR ( double x )

Calculates the SQuaRe of 'double' x, returning 'double'.

Definition at line 338 of file utils.h.

Referenced by add_dpd_thermo_pair_force(), add_force_contribution(), add_gaussian_pair_force(), add_inter_dpd_pair_force(), add_kinetic_energy(), add_kinetic_virials(), add_lj_pair_force(), add_ljangle_pair_force(), add_ljcos2_pair_force(), add_ljcos_pair_force(), add_rod_force(), add_SmSt_pair_force(), angle_cosine_energy(), angle_cossquare_energy(), angle_energy(), angle_harmonic_energy(), angledist_energy(), buf_mindist4(), build_verlet_lists(), build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calc_angle_3body_forces(), calc_angle_3body_tabulated_forces(), calc_angle_cosine_3body_forces(), calc_angle_cosine_force(), calc_angle_cossquare_3body_forces(), calc_angle_force(), calc_angle_harmonic_3body_forces(), calc_bond_dist(), calc_bond_dist_av(), calc_bond_l(), calc_bond_l_av(), calc_buck_cap_radii(), calc_endangledist_pair_force(), calc_g123(), calc_g1_av(), calc_g2_av(), calc_g3_av(), calc_internal_dist(), calc_internal_dist_av(), calc_kinetic(), calc_link_cell_iccp3m(), calc_lj_cap_radii(), calc_ljangle_cap_radii(), calc_ljcos2_cap_radii(), calc_local_temp(), calc_part_distribution(), calc_re(), calc_re_av(), calc_rg(), calc_rg_av(), calc_scaling(), calc_scaling2(), calc_self_energy_coeffs(), calc_subt_lj_pair_force(), calc_wallbondyz(), calc_wallmsdx(), calc_wallmsdyz(), calc_wallrdfyz(), calculate_cylinder_dist(), calculate_maze_dist(), calculate_plane_dist(), calculate_pore_dist(), calculate_sphere_dist(), check_resort_particles(), dipole_energy(), distance(), distance2(), distance2vec(), distto(), dp3m_average_dipolar_self_energy(), dp3m_calc_influence_function_energy(), dp3m_calc_influence_function_force(), dp3m_calc_kspace_forces(), dp3m_count_magnetic_particles(), dp3m_get_accuracy(), dp3m_k_space_error(), dp3m_perform_aliasing_sums_energy(), dp3m_perform_aliasing_sums_force(), dp3m_tune_aliasing_sums(), ELC_add_force(), ELC_energy(), ELC_P3M_modify_p3m_sums_both(), ELC_P3M_modify_p3m_sums_image(), ELC_P3M_restore_p3m_sums(), ELC_set_params(), ELC_tune(), endangledist_pair_energy(), energy_contribution(), fene_set_params(), finalize_p_inst_npt(), force_and_velocity_check(), gaussian_pair_energy(), get_mol_dist(), get_mol_dist_partcfg(), get_nonbonded_interaction(), harmonic_pair_energy(), icosaederC(), init_ghost_force(), init_local_particle_force(), integrate_vv(), lb_calc_local_fields(), lb_reinit_parameters(), lb_relax_modes(), lj_cos_set_params(), lj_pair_energy(), ljangle_pair_energy(), ljcos2_pair_energy(), ljcos_pair_energy(), maggs_add_transverse_field(), maggs_calc_init_e_field(), maggs_electric_energy(), maggs_magnetic_energy(), maxwell_velocitiesC(), mindist(), mindist3(), mindist4(), MMM1D_init(), MMM1D_set_params(), mmm1d_tune(), MMM2D_add_far(), MMM2D_self_energy(), MMM2D_set_params(), MMM2D_tune_far(), MMM2D_tune_near(), normr(), p3m_analytic_cotangent_sum(), p3m_caf(), p3m_calc_dipole_term(), p3m_calc_influence_function_force(), p3m_calc_kspace_forces(), p3m_calc_kspace_stress(), p3m_count_charged_particles(), p3m_get_accuracy(), p3m_k_space_error(), p3m_perform_aliasing_sums_energy(), p3m_perform_aliasing_sums_force(), p3m_real_space_error(), p3m_tune_aliasing_sums(), polymerC(), propagate_press_box_pos_and_rescale_npt(), propagate_vel(), rescale_forces_propagate_vel(), rod_energy(), sinc(), sqrlen(), subt_lj_pair_energy(), subt_lj_set_params(), tab_bond_energy(), tabulated_pair_energy(), tclcommand_analyze_parse_necklace(), tclcommand_analyze_parse_Vkappa(), tclcommand_constraint_parse_cylinder(), tclcommand_constraint_parse_pore(), tclcommand_constraint_parse_wall(), tclcommand_lbboundary_cylinder(), tclcommand_lbboundary_pore(), tclcommand_lbboundary_wall(), unfolded_distance(), vec_rotate(), and velocitiesC().

MDINLINE double sqrlen ( double v[3] )

calculates the squared length of a vector

Definition at line 436 of file utils.h.

References i, and SQR().

Referenced by add_ljangle_pair_force(), angle_btw_triangles(), angle_cosine_energy(), angle_cossquare_energy(), angle_energy(), angle_harmonic_energy(), angledist_energy(), bilayer_density_profile_sphere(), calc_angle_3body_forces(), calc_angle_3body_tabulated_forces(), calc_angle_cosine_3body_forces(), calc_angle_cosine_force(), calc_angle_cossquare_3body_forces(), calc_angle_cossquare_force(), calc_angle_force(), calc_angle_harmonic_3body_forces(), calc_angle_harmonic_force(), calc_angledist_force(), calc_angledist_param(), calc_dihedral_angle(), calc_endangledist_pair_force(), calc_energy_kinetic_mol(), calc_fene_pair_force(), calc_force_between_mol(), calc_harmonic_pair_force(), calc_mol_gyr_radius2(), calc_mol_hydro_radius(), calc_overlap_angle_force(), calc_overlap_bond_force(), calc_pwangle(), calc_radial_density_map(), calc_stretching_force_pair_force(), calc_subt_lj_pair_force(), calc_tab_angle_force(), calc_tab_bond_force(), compute_pos_corr_vec(), distribute_mol_force(), distto(), ELC_P3M_dielectric_layers_energy_contribution(), ELC_P3M_dielectric_layers_energy_self(), ELC_P3M_dielectric_layers_force_contribution(), ELC_P3M_self_forces(), fene_pair_energy(), harmonic_pair_energy(), integrate_reaction(), layered_calculate_energies(), layered_calculate_ia(), layered_calculate_ia_iccp3m(), layered_calculate_virials(), ljangle_pair_energy(), meta_perform(), min_distance2(), MMM2D_dielectric_layers_energy_contribution(), MMM2D_dielectric_layers_force_contribution(), nbhood(), nsq_calculate_energies(), nsq_calculate_ia(), nsq_calculate_ia_iccp3m(), nsq_calculate_virials(), overlap_angle_energy(), overlap_bond_energy(), polymerC(), print_bond_len(), subt_lj_pair_energy(), tab_angle_energy(), tab_bond_energy(), tclcommand_analyze_parse_and_print_energy_kinetic(), test_mesh_elements(), unit_vector(), update_mol_pos_particle(), update_mol_vel_particle(), and vs_relate_to().

MDINLINE char* strcat_alloc	(	char *	left,
		char *	right
	)

extend a string with another one.

Like strcat, just automatically increases the string space

Definition at line 919 of file utils.h.

References malloc, and realloc.

Referenced by dp3m_adaptive_tune(), dp3m_mc_time(), mmm1d_tune(), p3m_adaptive_tune(), and p3m_mc_time().

MDINLINE double unfolded_distance	(	double	pos1[3],
		int	image_box1[3],
		double	pos2[3],
		int	image_box2[3],
		double	box_l[3]
	)

returns the distance between the unfolded coordintes of two particles.

Parameters:

pos1	Position of particle one.
image_box1	simulation box index of particle one .
pos2	Position of particle two.
image_box2	simulation box index of particle two .
box_l	size of simulation box.